org.biojava.nbio.structure.align.multiple

Interface Block

All Superinterfaces:

ScoresCache

All Known Implementing Classes:

BlockImpl

public interface Block
extends ScoresCache

A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a sequential order.

A collection of Blocks, named BlockSet, allows the description of circular permutations (CP) and non-topological alignments.

Every Block object is part of a BlockSet instance, its parent, which has in turn a MultipleAlignment instance as parent.

Since:

4.1.0

Author:

Aleix Lafita, Spencer Bliven

Method Summary

Modifier and Type	Method and Description
void	clear() Clear scores and other properties which depend on the specific alignment.
Block	clone() Creates and returns an identical copy of this block.
List<List<Integer>>	getAlignRes() Returns the double List containing the aligned residues for each structure.
List<Integer>	getAlignResCounts() Returns the number of non null positions (residues) of each structure in the alignment Block.
BlockSet	getBlockSet() Returns the parent BlockSet of the Block.
int	getCoreLength() Returns the number of aligned positions (columns) without gaps in the Block.
int	getFinalIndex(int str) Calculates and returns the last position of the specified structure in the alignment that is not null.
int	getFinalResidue(int str) Calculates and returns the last residue of the specified structure in the alignment that is not null.
int	getStartIndex(int str) Calculates and returns the first position of the specified structure in the alignment that is not null.
int	getStartResidue(int str) Calculates and returns the first residue of the specified structure in the alignment that is not null.
int	length() Returns the total number of aligned positions (columns) in the Block.
void	setAlignRes(List<List<Integer>> alignRes) Set the double List containing the aligned residues for each structure.
void	setBlockSet(BlockSet parent) Set the back-reference to its parent BlockSet.
int	size() Returns the number of aligned structures (rows) in the Block.

Methods inherited from interface org.biojava.nbio.structure.align.multiple.ScoresCache

getScore, getScores, putScore

Method Detail

clone

Block clone()

Creates and returns an identical copy of this block.

Returns:

Block identical copy of this object.

setBlockSet

void setBlockSet(BlockSet parent)

Set the back-reference to its parent BlockSet.

Parameters:

parent - the parent BlockSet.

See Also:

getBlockSet()

getBlockSet

BlockSet getBlockSet()

Returns the parent BlockSet of the Block. Returns null if there is no referenced object.

Returns:

BlockSet the parent BlockSet of the Block, or null.

See Also:

setBlockSet(BlockSet)

getAlignRes

List<List<Integer>> getAlignRes()

Returns the double List containing the aligned residues for each structure.

alignRes.get(structure).get(residue) = alignRes.get(size).get(length).

Returns:

List a double List of aligned residues for each structure.

See Also:

#setAlignRes()

setAlignRes

void setAlignRes(List<List<Integer>> alignRes)

Set the double List containing the aligned residues for each structure.

Parameters:

alignRes - a double List of Integers with the aligned residues.

See Also:

getAlignRes()

length

int length()

Returns the total number of aligned positions (columns) in the Block.

Returns:

int number of aligned residues.

See Also:

getCoreLength();, size()

size

int size()

Returns the number of aligned structures (rows) in the Block.

Returns:

int number of aligned structures.

See Also:

length(), getCoreLength()

getCoreLength

int getCoreLength()

Returns the number of aligned positions (columns) without gaps in the Block.

Returns:

int number of aligned residues.

See Also:

#updateCoreLength(), length(), size()

getAlignResCounts

List<Integer> getAlignResCounts()

Returns the number of non null positions (residues) of each structure in the alignment Block. The values can be used to compute the coverages.

Returns:

List of residue counts for each structure

getStartIndex

int getStartIndex(int str)

Calculates and returns the first position of the specified structure in the alignment that is not null. This will return the aligment index, not the reisude aligned in that position.

Parameters:

str - structure index

Returns:

the first non null aligned position of the structure

getStartResidue

int getStartResidue(int str)

Calculates and returns the first residue of the specified structure in the alignment that is not null. This will return the aligned residue, not the alignment index.

Parameters:

str - structure index

Returns:

the first non null aligned residue of the structure

getFinalIndex

int getFinalIndex(int str)

Calculates and returns the last position of the specified structure in the alignment that is not null. This will return the aligment index, not the reisude aligned in that position.

Parameters:

str - structure index

Returns:

the last non null aligned position of the structure

getFinalResidue

int getFinalResidue(int str)

Calculates and returns the last residue of the specified structure in the alignment that is not null. This will return the aligned residue, not the alignment index.

Parameters:

str - structure index

Returns:

the last non null aligned residue of the structure

clear

void clear()

Clear scores and other properties which depend on the specific alignment. This frees memory and ensures consistency of the cached variables.